Partial ORF1ab Gene Target Failure with Omicron BA.2.12.1

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1. Version published to 10.1128/jcm.00600-22

   Jun 15, 2022
2. 

   ScreenIT

   Apr 30, 2022

   SciScore for 10.1101/2022.04.25.22274187: (What is this?)

   Please note, not all rigor criteria are appropriate for all manuscripts.

   Table 1: Rigor

   Ethics	not detected.
   Sex as a biological variable	not detected.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.

   Table 2: Resources

   Software and Algorithms
   Sentences	Resources
   Samples sent for SARS-CoV-2 WGS may have been tested on a variety of other FDA EUA-approved SARS-CoV-2 diagnostic platforms, and not a cobas® SARS-CoV-2 assay, depending on workflows and testing protocols of the originating laboratory.	SARS-CoV-2 suggested: (Active Motif Cat# 91351, RRID:AB_2847848) WGS suggested: None
   Sequence reads were mapped to reference genome Wuhan-Hu-1 (NC_045512.2) using BWA (version 0.7.15), variant calling was performed with both Freebayes (version 1.3.4) and LoFreq (version 2.1.5).	BWA

   SciScore for 10.1101/2022.04.25.22274187: (What is this?)

   Please note, not all rigor criteria are appropriate for all manuscripts.

   Table 1: Rigor

   Ethics	not detected.
   Sex as a biological variable	not detected.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.

   Table 2: Resources

   Software and Algorithms
   Sentences	Resources
   Samples sent for SARS-CoV-2 WGS may have been tested on a variety of other FDA EUA-approved SARS-CoV-2 diagnostic platforms, and not a cobas® SARS-CoV-2 assay, depending on workflows and testing protocols of the originating laboratory.	SARS-CoV-2 suggested: (Active Motif Cat# 91351, RRID:AB_2847848) WGS suggested: None
   Sequence reads were mapped to reference genome Wuhan-Hu-1 (NC_045512.2) using BWA (version 0.7.15), variant calling was performed with both Freebayes (version 1.3.4) and LoFreq (version 2.1.5).	BWA suggested: (BWA, RRID:SCR_010910) Freebayes suggested: (FreeBayes, RRID:SCR_010761) LoFreq suggested: (LoFreq, RRID:SCR_013054)
   Genomic data from CUIMC is routinely uploaded to GISAID and to GenBank (under NCBI BioProject PRJNA751551).	BioProject suggested: None
   Data Analysis: All charts and analyses were generated and performed with GraphPad Prism v8.2.1.	GraphPad Prism suggested: (GraphPad Prism, RRID:SCR_002798)

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   Results from OddPub: Thank you for sharing your code and data.

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   Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

   This study has some limitations. Not all SARS-CoV-2 tests were performed on the cobas® SARS-CoV-2 assays as multiple NAAT platforms are used at each participating site, and operational workflow may have unintentionally introduced biases (e.g., directing samples from certain patient populations or need for rapid result to particular platforms) to the study set. All analyses were performed on a per-sample and not a per-subject basis, and a single subject’s samples could have been included multiple times within the data set. However, the impact of this possibility is diminished by the multi-center nature of this study and large data. While pOGTF is currently specific to BA.2.12.1, the specificity, sensitivity, and predictive values may change over time as SARS-CoV-2 continues to evolve and the lineages prevalent in the population changes. Although pOGTF can be a rapid and useful tool for monitoring BA.2.12.1, WGS remains important in confirming the lineage, assessing for additional mutations, and detecting new variants that decrease the specificity of the association of pOGTF with BA.2.12.1.

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   Results from TrialIdentifier: No clinical trial numbers were referenced.

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   Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

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   Results from JetFighter: We did not find any issues relating to colormaps.

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   Results from rtransparent:

   • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
   • Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
   • No protocol registration statement was detected.

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   Results from scite Reference Check: We found no unreliable references.

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   Read the original source
3. 

   Version published to 10.1101/2022.04.25.22274187v1 on medRxiv

   Apr 28, 2022